1. Field of the Invention
The present invention relates to a method and apparatus for determining the specificity of a candidate probe sequence.
2. Description of the Related Art
The interest in microarrays using oligonucleotides has greatly increased because a small number of experiments performed with such devices can produce a large amount of biological information. A microarray immobilizes oligonucleotides on a substrate which can function as probes. The probes on the microarray can then hybridize to a nucleic acid from which biological information is to be obtained, and the degree of hybridization can be measured, thereby obtaining biological information. Such microarrays can be applied in identifying gene expression, identifying specific gene information of a genome, and detecting pathogens.
One of the most important processes for preparing a microarray is the selection of an effective probe. In general, a suitable probe can be selected by predetermining the hybridization strength between a nucleic acid in a sample and the potential probe to be hybridized thereto. However, because information on nucleic acid sequences is not known for all species and some species exist which have similar nucleic acid sequences, selecting a probe is not always a simple process.
For example, when detecting pathogens in a sample, even if the presence of one kind of pathogen is detected and identified, different kinds of pathogens may actually coexist in the sample. In particular, multiple pathogens may coexist in applications such as predicting diseases or detecting food poisoning bacteria. Therefore, selecting a probe which hybridizes specifically with a particular pathogen, or class of pathogens, and hybridizes non-specifically to other pathogens is important for such applications.
Although these concerns are considered mainly in the initial stage of designing a probe, designing a probe using all known genes of bacteria or other pathogens is impossible and inefficient. However, if there is no consideration as to whether a candidate probe will simultaneously detect a target pathogen as well as other non-target pathogens, a large number of experimental errors may occur. Accordingly, a prior art process of designing a probe involves first designing the probe to hybridize with a limited number of major pathogens, and then experimentally determining whether the major pathogens are detected by the probe in samples.
Although such a probe selecting method including experimental detection can easily yield a probe that can hybridize to a target pathogen, using such a method to select a probe which is specific for the target pathogen, but non-specific for related pathogensis difficult, and requires an increase in time and cost in selecting the probe.
Factors that must be considered in designing a probe have changed, and their number has increased. For example, gene sequences are being updated on a daily basis, new species of bacteria and other pathogens are being found, and the taxonomic classification system of species is changing. Also, gene expression information and phylogenetic trees for species are being updated. Therefore, if a probe prepared one year ago is used this year, the validity of the specificity of the probe may not be guaranteed. Consequently, there is a need to check the specificity of previously designed probes or microarrays.